New approaches to DNA sequencing are required to reduce costs and increase the availability of personalized genomics (M. Zwolak, M. Di Ventra, Reviews of Modern Physics 80, 141 (2008)). In addition, long contiguous reads would help to unravel the long-range structure of the genome (E. Pennish, Science 318, 1842 (2007); A. J. Sharp, et al., Annu. Rev. Genomic Hum. Genet. ARJ, 407 (2006). In contrast to Sanger sequencing and next-generation methods, nanopore sequencing (D. Branton et al., Nature Biotechnology 26, 1146 (2008)) is an enzyme-free technique in which DNA molecules are forced through a tiny aperture using electrophoresis, so that a sequence-reading mechanism could maintain its fidelity over the entire length of a molecule. Ion current that passes through the pore is sensitive to the sequence in the nanopore (M. Akeson, et al., Biophys J. 77, 3227 (1999); A. Meller, et al., Proc. Natl. Acad. Sci. (USA) 97, 1079 (2000); N. Ashkenasy, et al., Angew. Chem. Int. Ed. 44, 1401 (2005)) but all of the bases in the nanopore channel contribute to the current blockade (A. Meller, et al., Phys. Rev. Lett. 86, 3435 (2001)) as well as those in the region of high field beyond the pore (A. Aksimentiev, et al., Biophysical Journal 87, 2086 (September, 2004); M. Muthukumar, et al., Proc. Natl. Acad. Sci. (USA) 103, 5273 (2006)). In consequence, single base resolution has not yet been attained with an ion current readout. Lee and Thundat proposed that electron tunneling across a DNA molecule might be localized enough to sense and identify single nucleotides (J. W. Lee, and T. Thundat. U.S. Pat. No. 6,905,586 (2005)), a conjecture supported by the calculations of Zwolak and Di Ventra (M. Zwolak, M. Di Ventra, Nano Lett. 5, 421 (2005)). Further calculations show that thermal motion of molecules in the gap broadens the distribution of tunnel currents (J. Lagerqvist, et al., Biophys J. 93, 2384 (2007); R. Zikic et al., Phys. Rev. E 74, 011919 1 (2006)), reducing selectivity substantially. The range of orientations of molecules in a tunnel gap can be greatly reduced by using chemical bonds to tether it to the readout electrodes (X. D. Cui et al., Science 294, 571 (2001)), however, the use of strong bonds is not an option for DNA sequencing where the contact to the electrodes must slide from one nucleotide to the next rapidly. Ohshiro and Umezawa demonstrated that hydrogen bonds can be used to provide chemical contrast in scanning tunneling microscope images (T. Ohshiro, Y. Umezawa, Proc. Nat. Acad. Sci. 103, 10 (2006)) suggesting that these weaker bonds can serve as “sliding contacts” to single molecules.
In applications W02008124706A2 (“Sequencing by Recognition”), 61/037,647 (Nanotube Nanopore for DNA Sequencing”), 61/083,001) (“Tandem Reader for DNA Sequencing.”) 61/083,993 (“Carbon Nanotube Based Device for Sequencing Polymers”), 61/103,019 (“A Trans-base tunnel Reader for Sequencing”), all of which are incorporated by reference, schemes for contacting target bases in DNA in a tunnel gap with electrodes functionalized with reagents designed to hydrogen bond specifically to one base or another are described. In consequence, a different reader is required for each DNA base, so that a sequence has to be assembled by aligning the output of four separate readers. Furthermore, the reliance on reagents designed to target a specific site means that when two different sites are targeted (one by each electrode) the electrodes have to be functionalized independently, which is difficult to achieve in a nanoscale gap.